Bipartite graphs in R

Registered by Gábor Csárdi on 2012-09-01

What to do to handle bipartite graphs better.

Blueprint information

Status:
Not started
Approver:
None
Priority:
Undefined
Drafter:
None
Direction:
Needs approval
Assignee:
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Definition:
Drafting
Series goal:
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Implementation:
Unknown
Milestone target:
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Bipartite warnings
------------------------
Look over all functions and add warnings for the ones that should behave differently for bipartite graphs, but they don't. This is a huge task....

Configure bipartite warnings
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Add an option, to optionally suppress the warnings introduced in 1. It is not yet decided whether these warnings should be on by default or not.

Add a function to export bipartite Pajek graphs.
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https://bugs.launchpad.net/igraph/+bug/1044881
We already have a function to read bipartite Pajek graphs. Writing them is a bit more difficult, because we might need to reorder the vertices, since Pajek needs vertices to be sorted according to their types.

Bipartite layouts
----------------------
https://bugs.launchpad.net/igraph/+bug/1044984
Add some layout function(s) specifically for bipartite graphs.
See http://www.iplab.cs.tsukuba.ac.jp/paper/.../ito_hcii2009.pdf

Bipartite modularity
--------------------------
https://bugs.launchpad.net/igraph/+bug/594581

1 Michael J Barber: Modularity and community detection in bipartite networks,
Phys Rev E 76 066102
http://pre.aps.org/abstract/PRE/v76/i6/e066102

2 Roger Guimerà, Marta Sales-Pardo, and Luís A. Nunes Amaral
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17930301

3 http://dl.acm.org/citation.cfm?id=1557914.1557956

Community detection
----------------------------
1 Module identification in bipartite and directed networks
Roger Guimerà, Marta Sales-Pardo, and Luís A. Nunes Amaral
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17930301

2 Michael J Barber: Modularity and community detection in bipartite networks,
Phys Rev E 76 066102
http://pre.aps.org/abstract/PRE/v76/i6/e066102

DONE Erdős-Rényi type bipartite generator
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https://bugs.launchpad.net/igraph/+bug/1044884

Bipartite configuration model sampler
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https://bugs.launchpad.net/igraph/+bug/667661
http://dx.doi.org/10.1016/j.physa.2006.04.047

Bipartite transitivity
-------------------------
https://bugs.launchpad.net/igraph/+bug/727516

Consider adding to igraph the computation of bipartite clustering coefficients as defined in pp 40-41 of Latapy et al (2008). Find attached a python implementation with some tests.

Matthieu Latapy, Clémence Magnien and Nathalie Del Vecchio. Basic Notions for the Analysis of Large Two-mode Networks. Social Networks 30 (1), p. 31-48, 2008
There is also a C implementation from the authors: http://www-rp.lip6.fr/~latapy/Bip/

(?)

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